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  • 1
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    Using hydrogeochemical signatures of stream water to assess pathways for rainfall events: towards a predictive model (2013)
    Wiley
    Details
    Publication Date: 2013-03-05
    Description: Thanks to its simple division into agricultural and forestry land use, the Corbeira catchment (Galicia, Spain) is used as a case study to build a predictive model using hydrogeochemical signatures. Stream data acquired under recessional flow conditions over a one year period were obtained from a sampling station near the downstream end of the catchment, and using principal component analysis it is shown hat some of the analytical parameters are covariant and some are negatively correlated. These findings support inferences about the pathways of rainfall in the catchment. Specific signatures may be associated with the dominant hydrological source, either surface runoff or subsurface waters: additionally, the dominant land use in that part of the catchment, where the flow originated can also be predicted. The dominant runoff shows a strong covariance between suspended solids (SS) and particulate phosphorus (PP), with a clear negative correlation with pH. Dissolved organic carbon (DOC) data are associated with this covariant set when these compounds are available in the soils in question. Dissolved phosphorus, total organic nitrogen and dissolved nitrates are also associated with the same covariant set when the runoff flows through areas of extensive agricultural use. The SS − PP covariance is less significant at lower flows. Typical base flow regimes show a significant covariance between salinity and pH, with a marked negative correlation with SS − PP set, confirming the dominance of subsurface waters in the baseflow, as expected. Seasonally divergent DOC − SS behavior proves to be a useful tracer for rainfall regimes. The DOC trend shows a sinusoidal annual variation in amplitude, determined by the rainfall regime. As a result, flow from the catchment is dominated by surface water whenever there is synchronicity between the peaks of DOC and SS. Copyright © 2013 John Wiley & Sons, Ltd.
    Print ISSN: 0885-6087
    Electronic ISSN: 1099-1085
    Topics: Architecture, Civil Engineering, Surveying , Geography
    Published by Wiley
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  • 2
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    Use of ChIP-Seq data for the design of a multiple promoter-alignment method (2012)
    Oxford University Press
    Details
    Publication Date: 2012-04-15
    Description: We address the challenge of regulatory sequence alignment with a new method, Pro-Coffee, a multiple aligner specifically designed for homologous promoter regions. Pro-Coffee uses a dinucleotide substitution matrix estimated on alignments of functional binding sites from TRANSFAC. We designed a validation framework using several thousand families of orthologous promoters. This dataset was used to evaluate the accuracy for predicting true human orthologs among their paralogs. We found that whereas other methods achieve on average 73.5% accuracy, and 77.6% when trained on that same dataset, the figure goes up to 80.4% for Pro-Coffee. We then applied a novel validation procedure based on multi-species ChIP-seq data. Trained and untrained methods were tested for their capacity to correctly align experimentally detected binding sites. Whereas the average number of correctly aligned sites for two transcription factors is 284 for default methods and 316 for trained methods, Pro-Coffee achieves 331, 16.5% above the default average. We find a high correlation between a method's performance when classifying orthologs and its ability to correctly align proven binding sites. Not only has this interesting biological consequences, it also allows us to conclude that any method that is trained on the ortholog data set will result in functionally more informative alignments.
    Keywords: Computational Methods, Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    pH and Particle Structure Effects on Silica Removal by Coagulation (2012)
    Wiley
    Details
    Publication Date: 2012-05-30
    Description: Coagulation is presented as an efficient alternative to reduce the silica content in effluents from recovered-paper mills that are intended to be recycled by a final reverse-osmosis (RO) step. Coagulation pretreatment by several polyaluminum chlorides (PACls) or FeCl 3 was optimized prior to the RO process. PACls with low alumina content and high basicity achieved almost a 100 % removal of silica at pH 10.5. A good reduction of the silica content was attained without regulating the pH by adding one of these PACls. Silica removal was related to the structure of the produced clots in which cylindrical particles produced higher silica removal. All coagulants removed more than 50 % of the chemical oxygen demand (COD). Coagulation is presented as an efficient technique to remove silica from paper mill effluents. Pretreatment by polyaluminum chlorides (PACls) and FeCl 3 was optimized prior to reverse osmosis. A higher silica removal was attained when cylindrical particles were formed. PACls with low alumina content and high basicity achieved almost 100 % removal of silica at pH 10.5.
    Print ISSN: 0930-7516
    Electronic ISSN: 1521-4125
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Published by Wiley
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  • 4
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    ReLA, a local alignment search tool for the identification of distal and proximal gene regulatory regions and their conserved transcription factor binding sites (2012)
    Oxford University Press
    Details
    Publication Date: 2012-03-20
    Description: Motivation: The prediction and annotation of the genomic regions involved in gene expression has been largely explored. Most of the energy has been devoted to the development of approaches that detect transcription start sites, leaving the identification of regulatory regions and their functional transcription factor binding sites (TFBSs) largely unexplored and with important quantitative and qualitative methodological gaps. Results: We have developed ReLA (for REgulatory region Local Alignment tool), a unique tool optimized with the Smith–Waterman algorithm that allows local searches of conserved TFBS clusters and the detection of regulatory regions proximal to genes and enhancer regions. ReLA's performance shows specificities of 81 and 50% when tested on experimentally validated proximal regulatory regions and enhancers, respectively. Availability: The source code of ReLA's is freely available and can be remotely used through our web server under http://www.bsc.es/cg/rela . Contact: david.torrents@bsc.es Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 5
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    Crystallization of CaCO3 in Water–Alcohol Mixtures: Spherulitic Growth, Polymorph Stabilization, and Morphology Change (2011)
    American Chemical Society (ACS)
    Details
    Publication Date: 2011-12-24
    Description: Crystal Growth & Design DOI: 10.1021/cg2012342
    Print ISSN: 1528-7483
    Electronic ISSN: 1528-7505
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by American Chemical Society (ACS)
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  • 6
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    Mesoscale Model to Select the Ideal Location for New Vineyard Plantations in the Rioja Qualified Denomination of Origin (2014)
    Hindawi
    Details
    Publication Date: 2014-10-17
    Description: La Rioja is the region where the top rated wines from Spain come from and also the origin of one of the most prestigious wines in the world. It is worldwide recognized, not only for the quality of the vine, but also for the many factors involved in the process that are controllable by the farmer, such as fertilizers, irrigation, etc. Likewise, there are other key factors, which cannot be controlled that play, however, a crucial role in the quality of the wine, such as temperature, radiation, humidity, and rainfall. This research is focused on two of these factors: temperature and irradiation. The objective of this paper is to be able to recognize these factors, so as to ensure a proper decision criterion when selecting the best location for new vineyard plantations. To achieve this objective, a mesoscale model MM5 is used, and its performance is assessed and compared using different parameters, from the grid resolution to the physical parameterization of the model. Finally, the study evaluates the impact of the different parameterizations and options for the simulation of meteorological variables particularly relevant when choosing new vineyard sites (rainfall frequency, temperature, and sun exposure).
    Electronic ISSN: 1537-744X
    Topics: Natural Sciences in General
    Published by Hindawi
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  • 7
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    South American giant short-faced bear (Arctotherium angustidens) diet: evidence from pathology, morphology, stable isotopes, and biomechanics. (2014)
    Paleontological Society
    Details
    Publication Date: 2014-11-15
    Description: A bstract Arctotherium angustidens Gervais and Ameghino, 1880 (the South American giant short-faced bear) is known for being the earliest (Ensenadan Age, early to middle Pleistocene) and largest (body mass over 1 ton) of five described Arctotherium species endemic to South America. Here we assess the diet of this bear from multiple proxies: morphology, biomechanics, dental pathology, stable isotopes and a previous study using geometric morphometric methodology. Results favor the idea of animal matter consumption, probably from large vertebrates in addition to vegetable matter consumption. Most probably, active hunting was not the unique strategy of this bear for feeding, since its large size and great power may have allowed him to fight for the prey hunted by other Pleistocene carnivores. However, scavenging over mega mammal carcasses was probably another frequent way of feeding. South American short-faced bears adjusted their size and modified their diet through Pleistocene times, probably as a response to the diversification of the carnivore guild (from the few precursory taxa that crossed the Panamanian Isthmus during the Great American Biotic Interchange).
    Print ISSN: 0022-3360
    Electronic ISSN: 1937-2337
    Topics: Geosciences
    Published by Paleontological Society
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  • 8
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    Ecosystem-Wide Impacts of Deforestation in Mangroves: The Urabá Gulf (Colombian Caribbean) Case Study (2012)
    International Scholarly Research Network (ISRN)
    Details
    Publication Date: 2012-08-01
    Description: Mangroves are ecologically important and extensive in the Neotropics, but they are visibly threatened by selective logging and conversion to pastures in the Southern Caribbean. The objective of this paper was to summarize the impacts of both threats on forest structure, species composition, aboveground biomass and carbon reservoir, species introgressions, and benthic fauna populations by collating past and current data and by using an interdisciplinary approach in the Urabá Gulf (Colombia) as a case study. Mangroves in the Eastern Coast have been decimated and have produced unskewed tree-diameter (DBH) distributions due to the overexploitation of Rhizophora mangle for poles (DBH range: 7–17 cm) and of Avicennia germinans for planks and pilings (DBH 〉40 cm). Selective logging increased the importance value of the light-tolerant white mangrove Laguncularia racemosa, also increasing biomass and carbon storage in this species, thus offsetting reductions in other species. Introgressions (cryptic ecological degradation) by L. racemosa and Acrostichum aureum (mangrove fern) and low densities of otherwise dominant detritivore snails (Neritina virginea) were observed in periurban basin mangroves. Finally, basin mangroves were more threatened than fringing mangroves due to their proximity to expanding pastures, villages, and a coastal city.
    Print ISSN: 2090-4614
    Electronic ISSN: 2090-4622
    Topics: Biology
    Published by International Scholarly Research Network (ISRN)
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  • 9
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    Ecosystem-Wide Impacts of Deforestation in Mangroves: The Urabá Gulf (Colombian Caribbean) Case Study (2012)
    International Scholarly Research Network (ISRN)
    Details
    Publication Date: 2012-08-16
    Description: Mangroves are ecologically important and extensive in the Neotropics, but they are visibly threatened by selective logging and conversion to pastures in the Southern Caribbean. The objective of this paper was to summarize the impacts of both threats on forest structure, species composition, aboveground biomass and carbon reservoir, species introgressions, and benthic fauna populations by collating past and current data and by using an interdisciplinary approach in the Urabá Gulf (Colombia) as a case study. Mangroves in the Eastern Coast have been decimated and have produced unskewed tree-diameter (DBH) distributions due to the overexploitation of Rhizophora mangle for poles (DBH range: 7–17 cm) and of Avicennia germinans for planks and pilings (DBH 〉40 cm). Selective logging increased the importance value of the light-tolerant white mangrove Laguncularia racemosa, also increasing biomass and carbon storage in this species, thus offsetting reductions in other species. Introgressions (cryptic ecological degradation) by L. racemosa and Acrostichum aureum (mangrove fern) and low densities of otherwise dominant detritivore snails (Neritina virginea) were observed in periurban basin mangroves. Finally, basin mangroves were more threatened than fringing mangroves due to their proximity to expanding pastures, villages, and a coastal city.
    Print ISSN: 2090-4614
    Electronic ISSN: 2090-4622
    Topics: Biology
    Published by International Scholarly Research Network (ISRN)
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  • 10
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    Ecosystem-Wide Impacts of Deforestation in Mangroves: The Urabá Gulf (Colombian Caribbean) Case Study (2013)
    International Scholarly Research Network (ISRN)
    Details
    Publication Date: 2013-01-22
    Description: Mangroves are ecologically important and extensive in the Neotropics, but they are visibly threatened by selective logging and conversion to pastures in the Southern Caribbean. The objective of this paper was to summarize the impacts of both threats on forest structure, species composition, aboveground biomass and carbon reservoir, species introgressions, and benthic fauna populations by collating past and current data and by using an interdisciplinary approach in the Urabá Gulf (Colombia) as a case study. Mangroves in the Eastern Coast have been decimated and have produced unskewed tree-diameter (DBH) distributions due to the overexploitation of Rhizophora mangle for poles (DBH range: 7–17 cm) and of Avicennia germinans for planks and pilings (DBH 〉40 cm). Selective logging increased the importance value of the light-tolerant white mangrove Laguncularia racemosa, also increasing biomass and carbon storage in this species, thus offsetting reductions in other species. Introgressions (cryptic ecological degradation) by L. racemosa and Acrostichum aureum (mangrove fern) and low densities of otherwise dominant detritivore snails (Neritina virginea) were observed in periurban basin mangroves. Finally, basin mangroves were more threatened than fringing mangroves due to their proximity to expanding pastures, villages, and a coastal city.
    Print ISSN: 2090-4614
    Electronic ISSN: 2090-4622
    Topics: Biology
    Published by International Scholarly Research Network (ISRN)
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